r-ahocorasicktrie

downloads

Aho-Corasick is an optimal algorithm for finding many keywords in a text. It can locate all matches in a text in O(N+M) time; i.e., the time needed scales linearly with the number of keywords (N) and the size of the text (M). Compare this to the naive approach which takes O(N*M) time to loop through each pattern and scan for it in the text. This implementation builds the trie (the generic name of the data structure) and runs the search in a single function call. If you want to search multiple texts with the same trie, the function will take a list or vector of texts and return a list of matches to each text. By default, all 128 ASCII characters are allowed in both the keywords and the text. A more efficient trie is possible if the alphabet size can be reduced. For example, DNA sequences use at most 19 distinct characters and usually only 4; protein sequences use at most 26 distinct characters and usually only 20. UTF-8 (Unicode) matching is not currently supported.

Home https://github.com/chambm/AhoCorasickTrie
Versions 0.1.0
License Apache License 2.0
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/r-ahocorasicktrie

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install r-ahocorasicktrie

and update with:

conda update r-ahocorasicktrie

docker

A Docker container is available at https://quay.io/repository/biocontainers/r-ahocorasicktrie.